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Detailed information for vg1220236732:

Variant ID: vg1220236732 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20236732
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

TACAACCTCTCGGAACACATGGCACAAACGCAAGAATGGCAACAATCTGCTGATGCTCAGTTCGCCAATTTCAACAACATGATGCAGCAACAGCACGATG[G/A]
CCTTCAAGCATACTTCCGCTTTCAGGGATTCAATCCTCATCCAGGACCCTGAGCGAAAGCCAAACTTGGGGGAAGATATCTCTACCCCCACTAAGGTAAC

Reverse complement sequence

GTTACCTTAGTGGGGGTAGAGATATCTTCCCCCAAGTTTGGCTTTCGCTCAGGGTCCTGGATGAGGATTGAATCCCTGAAAGCGGAAGTATGCTTGAAGG[C/T]
CATCGTGCTGTTGCTGCATCATGTTGTTGAAATTGGCGAACTGAGCATCAGCAGATTGTTGCCATTCTTGCGTTTGTGCCATGTGTTCCGAGAGGTTGTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.80%	14.50%	13.71%	37.94%	NA
All Indica	2759	16.00%	16.40%	18.70%	48.89%	NA
All Japonica	1512	70.50%	0.80%	4.83%	23.88%	NA
Aus	269	14.50%	65.80%	10.78%	8.92%	NA
Indica I	595	35.80%	10.60%	18.15%	35.46%	NA
Indica II	465	16.80%	12.70%	14.62%	55.91%	NA
Indica III	913	2.30%	21.50%	21.36%	54.87%	NA
Indica Intermediate	786	16.40%	17.20%	18.45%	47.96%	NA
Temperate Japonica	767	95.40%	0.00%	0.26%	4.30%	NA
Tropical Japonica	504	32.70%	2.00%	13.69%	51.59%	NA
Japonica Intermediate	241	70.10%	0.80%	0.83%	28.22%	NA
VI/Aromatic	96	12.50%	37.50%	20.83%	29.17%	NA
Intermediate	90	44.40%	10.00%	11.11%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220236732	G -> DEL	LOC_Os12g33500.1	N	frameshift_variant	Average:10.572; most accessible tissue: Callus, score: 27.815	N	N	N	N
vg1220236732	G -> A	LOC_Os12g33500.1	missense_variant ; p.Gly361Asp; MODERATE	nonsynonymous_codon ; G361D	Average:10.572; most accessible tissue: Callus, score: 27.815	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220236732	2.59E-17	2.17E-105	mr1334	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220236732	5.04E-07	4.05E-11	mr1334	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220236732	3.10E-07	2.92E-18	mr1334	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220236732	NA	9.95E-07	mr1403	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220236732	4.37E-22	9.88E-118	mr1334_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220236732	5.17E-12	1.62E-15	mr1334_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220236732	4.34E-07	2.66E-21	mr1334_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220236732	2.57E-09	4.91E-57	mr1991_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1220236732	6.75E-06	3.56E-11	mr1991_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251